I want to take a look on the pre-normalised data of some Affymetrix .CEL files (HuGene-1_0-st-v1, so no MM spots on the chip).
For this I have to combined/summarised low level probe intensity values into probe sets values (that map to genes). For comparison I provide the first line of the Expression set:

My conclusion is that (0),(2),(3) is the same. My question now is: Is (1) the best method to get the pre-normalised probe sets values? I am right that the expresso function in (2) perform normalisation although I use normalize=FALSE? Iam right that the values in (1) are also log2 values?
Thank you!

Due to my very limited experience with the affy package I won't directly answer your questions. But I would like to point out that the oligo package is an alternative that you could compare with your approach (1). What I would do to get summarized but not normalized or background corrected (log2 transformed) data is: